RE: issues with AutoPSF for a cyclodextrin

From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Fri Oct 30 2009 - 17:02:48 CDT

Hello Peter

I try to apply patches manually but I got the following message: "Resid missing from patch target 14ba. Molecule destroyed by fatal error."
Regarding coordinates you are right about the warnings:
First there is "Open coordinate file xxxx-pdb for writing.
Read PDB CONECT records .....
Warning I couldn't find the original pdb to assign connectivity. Using autogenerated connectivity only."
But the resulting xxx-temp.xbgf file produced at this stage is still containing th required coordinates
And then after pressing "Create chain" residues from the original PDB are being replaced by non-interconnected residues from the topology file. With this also atom names are changed to the names from topology and hence subsequently there are a lot of
"Warning: Failed to set coordinates for atom XX" where atom naming from the initial PDB is being used.
Is there anything I can do about this ?

Many thanks and kind regards
Vlad
 
> Date: Thu, 29 Oct 2009 20:31:00 -0400
> From: petefred_at_ks.uiuc.edu
> To: vchindea_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: issues with AutoPSF for a cyclodextrin
>
> Hi Vlad,
> autopsf does not do anything to automatically detect when arbitrary
> bonding patches should be applied (which would really be a complex
> problem). You can either apply the patches that you need manually
> through the patch dialogue, or alter the topology to make those bonds
> part of the residue definition.
> More information would be required to determine the lack of coordinates
> -- were there any warnings or errors while psfgen was running?
> Best,
> Peter
>
> CHINDEA Vlad wrote:
> > Dear NAMD users
> >
> > I am trying to build the PSF of a cyclodextrin starting from an X-ray
> > diffraction PDB with a bit of manual adjustment done (file attached).
> > I have used topology files top_all22_sugar.inp and/or
> > top_all36_carb.inp. When applying AutoPSF the 10 interconnected
> > glucose residues were replaced by 10 independent glucose molecules in
> > the resulting PSF and PSB although patches for alpha glycosidic bond
> > are available at least in top_all36_carb.inp. Also the PDB contains
> > only blank coordinates. What would be the reason and what can I do
> > about it ?
> >
> > I would like to mention that I have changed the name of the glucose
> > residue from AGLC to AGL in topology and PDB file as according to my
> > knowledge (PDB specs 3.20) residue names should have only 3 characters.
> >
> > Many thanks for your support
> > Best wishes
> > Vlad
> >
> > ------------------------------------------------------------------------
> > Windows Live: Make it easier for your friends to see what you’re up to
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> > <http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009>
>
                                               
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<br>Hello Peter<br><br>I try to apply patches manually but I got the following message: "Resid missing from patch target 14ba. Molecule destroyed by fatal error."<br>Regarding coordinates you are right about the warnings:<br>First there is "Open coordinate file xxxx-pdb for writing.<br>Read PDB CONECT records .....<br>Warning I couldn't find the original pdb to assign connectivity. Using autogenerated connectivity only."<br>But the resulting xxx-temp.xbgf file produced at this stage is still containing th required coordinates<br>And then after pressing "Create chain" residues from the original PDB are being replaced by non-interconnected residues from the topology file. With this also atom names are changed to the names from topology and hence subsequently there are a lot of<br>"Warning: Failed to set coordinates for atom XX" where atom naming from the initial PDB is being used.<br>Is there anything I can do about this ?<br><br>Many thanks and kind regards<br>Vlad<br>&nbsp;<br>&gt; Date: Thu, 29 Oct 2009 20:31:00 -0400<br>&gt; From: petefred_at_ks.uiuc.edu<br>&gt; To: vchindea_at_hotmail.com<br>&gt; CC: namd-l_at_ks.uiuc.edu<br>&gt; Subject: Re: namd-l: issues with AutoPSF for a cyclodextrin<br>&gt; <br>&gt; Hi Vlad,<br>&gt; autopsf does not do anything to automatically detect when arbitrary<br>&gt; bonding patches should be applied (which would really be a complex<br>&gt; problem). You can either apply the patches that you need manually<br>&gt; through the patch dialogue, or alter the topology to make those bonds<br>&gt; part of the residue definition.<br>&gt; More information would be required to determine the lack of coordinates<br>&gt; -- were there any warnings or errors while psfgen was running?<br>&gt; Best,<br>&gt; Peter<br>&gt; <br>&gt; CHINDEA Vlad wrote:<br>&gt; &gt; Dear NAMD users<br>&gt; &gt;<br>&gt; &gt; I am trying to build the PSF of a cyclodextrin starting from an X-ray<br>&gt; &gt; diffraction PDB with a bit of manual adjustment done (file attached).<br>&gt; &gt; I have used topology files top_all22_sugar.inp and/or<br>&gt; &gt; top_all36_carb.inp. When applying AutoPSF the 10 interconnected<br>&gt; &gt; glucose residues were replaced by 10 independent glucose molecules in<br>&gt; &gt; the resulting PSF and PSB although patches for alpha glycosidic bond<br>&gt; &gt; are available at least in top_all36_carb.inp. Also the PDB contains<br>&gt; &gt; only blank coordinates. What would be the reason and what can I do<br>&gt; &gt; about it ?<br>&gt; &gt;<br>&gt; &gt; I would like to mention that I have changed the name of the glucose<br>&gt; &gt; residue from AGLC to AGL in topology and PDB file as according to my<br>&gt; &gt; knowledge (PDB specs 3.20) residue names should have only 3 characters.<br>&gt; &gt;<br>&gt; &gt; Many thanks for your support<br>&gt; &gt; Best wishes<br>&gt; &gt; Vlad<br>&gt; &gt;<br>&gt; &gt; ------------------------------------------------------------------------<br>&gt; &gt; Windows Live: Make it easier for your friends to see what you’re up to<br>&gt; &gt; on Facebook.<br>&gt; &gt; &lt;http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009&gt;>&gt; <br> <br /><hr />Keep your friends updated— <a href='http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_5:092010' target='_new'>even when you’re not signed in.</a></body>
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